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An unusual two-strain cholera outbreak in Lebanon, 2022-2023: a genomic epidemiology study

Author

Listed:
  • Antoine Abou Fayad

    (American University of Beirut
    American University of Beirut
    World Health Organization (WHO) Collaborating Center for Reference and Research on Bacterial Pathogens)

  • Rayane Rafei

    (Lebanese University)

  • Elisabeth Njamkepo

    (Centre National de Référence des vibrions et du choléra)

  • Jana Ezzeddine

    (American University of Beirut
    American University of Beirut
    World Health Organization (WHO) Collaborating Center for Reference and Research on Bacterial Pathogens)

  • Hadi Hussein

    (American University of Beirut
    American University of Beirut
    World Health Organization (WHO) Collaborating Center for Reference and Research on Bacterial Pathogens)

  • Solara Sinno

    (World Health Organization)

  • Jose-Rita Gerges

    (American University of Beirut
    American University of Beirut
    World Health Organization (WHO) Collaborating Center for Reference and Research on Bacterial Pathogens)

  • Sara Barada

    (American University of Beirut
    American University of Beirut
    World Health Organization (WHO) Collaborating Center for Reference and Research on Bacterial Pathogens)

  • Ahmad Sleiman

    (American University of Beirut
    American University of Beirut
    World Health Organization (WHO) Collaborating Center for Reference and Research on Bacterial Pathogens)

  • Moubadda Assi

    (World Health Organization)

  • Maryo Baakliny

    (Ministry of Public Health)

  • Lama Hamedeh

    (American University of Beirut)

  • Rami Mahfouz

    (American University of Beirut)

  • Fouad Dabboussi

    (Lebanese University)

  • Rita Feghali

    (Rafik Hariri University Hospital)

  • Zeina Mohsen

    (Rafik Hariri University Hospital)

  • Alisar Rady

    (World Health Organization)

  • Nada Ghosn

    (Ministry of Public Health)

  • Firas Abiad

    (Ministry of Public Health)

  • Abdinasir Abubakar

    (World Health Organization)

  • Amal Barakat

    (Eastern Mediterranean Regional Office Cairo)

  • Nadia Wauquier

    (World Health Organisation)

  • Marie-Laure Quilici

    (Centre National de Référence des vibrions et du choléra)

  • Monzer Hamze

    (Lebanese University)

  • François-Xavier Weill

    (Centre National de Référence des vibrions et du choléra)

  • Ghassan M. Matar

    (American University of Beirut
    American University of Beirut
    World Health Organization (WHO) Collaborating Center for Reference and Research on Bacterial Pathogens)

Abstract

Cholera is a life-threatening gastrointestinal infection caused by a toxigenic bacterium, Vibrio cholerae. After a lull of almost 30 years, a first case of cholera was detected in Lebanon in October 2022. The outbreak lasted three months, with 8007 suspected cases (671 laboratory-confirmed) and 23 deaths. In this study, we use phenotypic methods and microbial genomics to study 34 clinical and environmental Vibrio cholerae isolates collected throughout this outbreak. All isolates are identified as V. cholerae O1, serotype Ogawa strains from wave 3 of the seventh pandemic El Tor (7PET) lineage. Phylogenomic analysis unexpectedly reveals the presence of two different strains of the seventh pandemic El Tor (7PET) lineage. The dominant strain has a narrow antibiotic resistance profile and is phylogenetically related to South Asian V. cholerae isolates and derived African isolates from the AFR15 sublineage. The second strain is geographically restricted and extensively drug-resistant. It belongs to the AFR13 sublineage and clusters with V. cholerae isolates collected in Yemen. In conclusion, the 2022-2023 Lebanese cholera outbreak is caused by the simultaneous introduction of two different 7PET strains. Genomic surveillance with cross-border collaboration is therefore crucial for the identification of new introductions and routes of circulation of cholera, improving our understanding of cholera epidemiology.

Suggested Citation

  • Antoine Abou Fayad & Rayane Rafei & Elisabeth Njamkepo & Jana Ezzeddine & Hadi Hussein & Solara Sinno & Jose-Rita Gerges & Sara Barada & Ahmad Sleiman & Moubadda Assi & Maryo Baakliny & Lama Hamedeh &, 2024. "An unusual two-strain cholera outbreak in Lebanon, 2022-2023: a genomic epidemiology study," Nature Communications, Nature, vol. 15(1), pages 1-10, December.
    • Handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-51428-0
    DOI: 10.1038/s41467-024-51428-0
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    References listed on IDEAS

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    1. Ankur Mutreja & Dong Wook Kim & Nicholas R. Thomson & Thomas R. Connor & Je Hee Lee & Samuel Kariuki & Nicholas J. Croucher & Seon Young Choi & Simon R. Harris & Michael Lebens & Swapan Kumar Niyogi &, 2011. "Evidence for several waves of global transmission in the seventh cholera pandemic," Nature, Nature, vol. 477(7365), pages 462-465, September.
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